Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study.

ABSTRACT: The precise kinetic pathways of peptide clustering and fibril formation are not fully understood. Here we study the initial clustering kinetics and transient cluster morphologies during aggregation of the heptapeptide fragment GNNQQNY from the yeast prion protein Sup35. We use a mid-resolution coarse-grained molecular dynamics model of Bereau and Deserno to explore the aggregation pathways from the initial random distribution of free monomers to the formation of large clusters. By increasing the system size to 72 peptides we could follow directly the molecular events leading to the formation of stable fibril-like structures. To quantify those structures we developed a new cluster helicity parameter. We found that the formation of fibril-like structures is a cooperative processes that requi

SUBMITTER: Szala-Mendyk B 

PROVIDER: S-EPMC7598727 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature